Dihedral debugging

Glycine tripeptide

Crude 50 ns simulation of Gly(3) in vacuum.

Ramachandran

gly3, no restraint
gly3, phi=-90 dphi=75, fc=10, kfac=2 restraint

Files

mdp file:

;
;	File 'gly3_fullmd__1287526816.mdp' was generated
;	By user: ms872 (1005)
;	On host: nursie
;	At date: Tue Oct 19 23:20:28 2010
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include                  = -I../top
; e.g.: -DI_Want_Cookies -DMe_Too
define                   = 

; RUN CONTROL PARAMETERS
integrator               = sd
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.002
nsteps                   = 25000000
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part          = 1
init_step                = 0
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                = 

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric                  = 0
ld-seed                  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol                    = 10
emstep                   = 0.01
; Max number of iterations in relax_shells
niter                    = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep                   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep               = 1000
nbfgscorr                = 10

; TEST PARTICLE INSERTION OPTIONS
rtpi                     = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 1000
nstvout                  = 1000
nstfout                  = 0
; Output frequency for energies to log file and energy file
nstlog                   = 1000
nstenergy                = 1000
; Output frequency and precision for xtc file
nstxtcout                = 1000
xtc-precision            = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc_grps                 = protein
; Selection of energy groups
energygrps               = 

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
periodic_molecules       = no
; nblist cut-off        
rlist                    = 0.8

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = cut-off
rcoulomb-switch          = 0
rcoulomb                 = 1.4
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 1
epsilon_rf               = 1
; Method for doing Van der Waals
vdwtype                  = cut-off
; cut-off lengths       
rvdw-switch              = 0
rvdw                     = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = No
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Seperate tables between energy group pairs
energygrp_table          = 
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent         = No

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm             = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii               = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                 = 2
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent       = 80
; Salt concentration in M for Generalized Born models
gb_saltconc              = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha             = 1
gb_obc_beta              = 0.8
gb_obc_gamma             = 4.85
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension       = 2.092

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
tcoupl                   = v-rescale
; Groups to couple separately
tc-grps                  = protein
; Time constant (ps) and reference temperature (K)
tau_t                    = 2
ref_t                    = 300
; Pressure coupling     
Pcoupl                   = no
Pcoupltype               = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p                    = 1
compressibility          = 
ref-p                    = 
; Scaling of reference coordinates, No, All or COM
refcoord_scaling         = No
; Random seed for Andersen thermostat
andersen_seed            = 815131

; OPTIONS FOR QMMM calculations
QMMM                     = no
; Groups treated Quantum Mechanically
QMMM-grps                = 
; QM method             
QMmethod                 = 
; QMMM scheme           
QMMMscheme               = normal
; QM basisset           
QMbasis                  = 
; QM charge             
QMcharge                 = 
; QM multiplicity       
QMmult                   = 
; Surface Hopping       
SH                       = 
; CAS space options     
CASorbitals              = 
CASelectrons             = 
SAon                     = 
SAoff                    = 
SAsteps                  = 
; Scale factor for MM charges
MMChargeScaleFactor      = 1
; Optimization of QM subsystem
bOPT                     = 
bTS                      = 

; SIMULATED ANNEALING  
; Type of annealing for each temperature group (no/single/periodic)
annealing                = 
; Number of time points to use for specifying annealing in each group
annealing_npoints        = 
; List of times at the annealing points for each group
annealing_time           = 
; Temp. at each annealing point, for each group.
annealing_temp           = 

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173528

; OPTIONS FOR BONDS    
constraints              = all-bonds
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
continuation             = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = no
; Relative tolerance of shake
shake-tol                = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter               = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle          = 30
; Convert harmonic bonds to morse potentials
morse                    = no

; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl           = 

; WALLS                
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall                    = 0
wall_type                = 9-3
wall_r_linpot            = -1
wall_atomtype            = 
wall_density             = 
wall_ewald_zfac          = 3

; COM PULLING          
; Pull type: no, umbrella, constraint or constant_force
pull                     = no

; NMR refinement stuff 
; Distance restraints type: No, Simple or Ensemble
disre                    = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting          = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed              = no
disre-fc                 = 1000
disre-tau                = 0
; Output frequency for pair distances to energy file
nstdisreout              = 100
; Orientation restraints: No or Yes
orire                    = no
; Orientation restraints force constant and tau for time averaging
orire-fc                 = 0
orire-tau                = 0
orire-fitgrp             = 
; Output frequency for trace(SD) and S to energy file
nstorireout              = 100
; Dihedral angle restraints: No or Yes
dihre                    = yes
dihre_fc                 = 10

; Free energy control stuff
free-energy              = no
init-lambda              = 0
delta-lambda             = 0
sc-alpha                 = 0
sc-power                 = 0
sc-sigma                 = 0.3
couple-moltype           = 
couple-lambda0           = vdw-q
couple-lambda1           = vdw-q
couple-intramol          = no

; Non-equilibrium MD stuff
acc-grps                 = 
accelerate               = 
freezegrps               = 
freezedim                = 
cos-acceleration         = 0
deform                   = 

; Electric fields      
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x                      = 
E-xt                     = 
E-y                      = 
E-yt                     = 
E-z                      = 
E-zt                     = 

; User defined thingies
user1-grps               = 
user2-grps               = 
userint1                 = 0
userint2                 = 0
userint3                 = 0
userint4                 = 0
userreal1                = 0
userreal2                = 0
userreal3                = 0
userreal4                = 0

top file (here with restraint - without is identical except it lacks the [ dihedral restraint ] section):

;
;	File 'gly3.top' was generated
;	By user: ms872 (1005)
;	On host: nursie
;	At date: Tue Oct 19 23:07:48 2010
;
;	This is your topology file
;	"Fresh Air, Green Hair" (Frank Black)
;
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1   opls_900      1    GLY      N      1       -0.9    14.0067   ; qtot -0.9
     2   opls_909      1    GLY     H1      1       0.36      1.008   ; qtot -0.54
     3   opls_909      1    GLY     H2      1       0.36      1.008   ; qtot -0.18
     4  opls_906B      1    GLY     CA      1       0.06     12.011   ; qtot -0.12
     5   opls_140      1    GLY    HA1      1       0.06      1.008   ; qtot -0.06
     6   opls_140      1    GLY    HA2      1       0.06      1.008   ; qtot 0
     7   opls_235      1    GLY      C      2        0.5     12.011   ; qtot 0.5
     8   opls_236      1    GLY      O      2       -0.5    15.9994   ; qtot 0
     9   opls_238      2    GLY      N      3       -0.5    14.0067   ; qtot -0.5
    10   opls_241      2    GLY      H      3        0.3      1.008   ; qtot -0.2
    11  opls_223B      2    GLY     CA      3       0.08     12.011   ; qtot -0.12
    12   opls_140      2    GLY    HA1      3       0.06      1.008   ; qtot -0.06
    13   opls_140      2    GLY    HA2      3       0.06      1.008   ; qtot 0
    14   opls_235      2    GLY      C      4        0.5     12.011   ; qtot 0.5
    15   opls_236      2    GLY      O      4       -0.5    15.9994   ; qtot 0
    16   opls_238      3    GLY      N      5       -0.5    14.0067   ; qtot -0.5
    17   opls_241      3    GLY      H      5        0.3      1.008   ; qtot -0.2
    18  opls_223B      3    GLY     CA      5       0.08     12.011   ; qtot -0.12
    19   opls_140      3    GLY    HA1      5       0.06      1.008   ; qtot -0.06
    20   opls_140      3    GLY    HA2      5       0.06      1.008   ; qtot 0
    21   opls_267      3    GLY      C      6       0.52     12.011   ; qtot 0.52
    22   opls_269      3    GLY     OT      6      -0.44    15.9994   ; qtot 0.08
    23   opls_268      3    GLY      O      6      -0.53    15.9994   ; qtot -0.45
    24   opls_270      3    GLY     HO      6       0.45      1.008   ; qtot 0



[ dihedral_restraints ]
; ai   aj    ak    al  type  label  phi  dphi  kfac  power
; phi C'(n-1) - N - CA - C' 
  7	9	11	14	1 	 1 	-90	75	2 	 1 	
  14	16	18	21	1 	 1 	-90	75	2 	 1 	


[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1 
    1     3     1 
    1     4     1 
    4     5     1 
    4     6     1 
    4     7     1 
    7     8     1 
    7     9     1 
    9    10     1 
    9    11     1 
   11    12     1 
   11    13     1 
   11    14     1 
   14    15     1 
   14    16     1 
   16    17     1 
   16    18     1 
   18    19     1 
   18    20     1 
   18    21     1 
   21    22     1 
   21    23     1 
   23    24     1 

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     8     1 
    1     9     1 
    2     5     1 
    2     6     1 
    2     7     1 
    3     5     1 
    3     6     1 
    3     7     1 
    4    10     1 
    4    11     1 
    5     8     1 
    5     9     1 
    6     8     1 
    6     9     1 
    7    12     1 
    7    13     1 
    7    14     1 
    8    10     1 
    8    11     1 
    9    15     1 
    9    16     1 
   10    12     1 
   10    13     1 
   10    14     1 
   11    17     1 
   11    18     1 
   12    15     1 
   12    16     1 
   13    15     1 
   13    16     1 
   14    19     1 
   14    20     1 
   14    21     1 
   15    17     1 
   15    18     1 
   16    22     1 
   16    23     1 
   17    19     1 
   17    20     1 
   17    21     1 
   18    24     1 
   19    22     1 
   19    23     1 
   20    22     1 
   20    23     1 
   22    24     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     3     1 
    2     1     4     1 
    3     1     4     1 
    1     4     5     1 
    1     4     6     1 
    1     4     7     1 
    5     4     6     1 
    5     4     7     1 
    6     4     7     1 
    4     7     8     1 
    4     7     9     1 
    8     7     9     1 
    7     9    10     1 
    7     9    11     1 
   10     9    11     1 
    9    11    12     1 
    9    11    13     1 
    9    11    14     1 
   12    11    13     1 
   12    11    14     1 
   13    11    14     1 
   11    14    15     1 
   11    14    16     1 
   15    14    16     1 
   14    16    17     1 
   14    16    18     1 
   17    16    18     1 
   16    18    19     1 
   16    18    20     1 
   16    18    21     1 
   19    18    20     1 
   19    18    21     1 
   20    18    21     1 
   18    21    22     1 
   18    21    23     1 
   22    21    23     1 
   21    23    24     1 

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    2     1     4     5     3 
    2     1     4     6     3 
    2     1     4     7     3 
    3     1     4     5     3 
    3     1     4     6     3 
    3     1     4     7     3 
    1     4     7     8     3 
    1     4     7     9     3 
    5     4     7     8     3 
    5     4     7     9     3 
    6     4     7     8     3 
    6     4     7     9     3 
    4     7     9    10     3 
    4     7     9    11     3 
    8     7     9    10     3 
    8     7     9    11     3 
    7     9    11    12     3 
    7     9    11    13     3 
    7     9    11    14     3 
   10     9    11    12     3 
   10     9    11    13     3 
   10     9    11    14     3 
    9    11    14    15     3 
    9    11    14    16     3 
   12    11    14    15     3 
   12    11    14    16     3 
   13    11    14    15     3 
   13    11    14    16     3 
   11    14    16    17     3 
   11    14    16    18     3 
   15    14    16    17     3 
   15    14    16    18     3 
   14    16    18    19     3 
   14    16    18    20     3 
   14    16    18    21     3 
   17    16    18    19     3 
   17    16    18    20     3 
   17    16    18    21     3 
   16    18    21    22     3 
   16    18    21    23     3 
   19    18    21    22     3 
   19    18    21    23     3 
   20    18    21    22     3 
   20    18    21    23     3 
   18    21    23    24     3 
   22    21    23    24     3 

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3
    4     9     7     8     1    improper_O_C_X_Y
    7    11     9    10     1    improper_Z_N_X_Y
   11    16    14    15     1    improper_O_C_X_Y
   14    18    16    17     1    improper_Z_N_X_Y
   18    22    21    23     1    improper_O_C_X_Y

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound        #mols
Protein             1